Fig. 1.

The workflow of MSP-HTPrimer pipeline. The MSP-HTPrimer pipeline can be run via an intuitive web interface. The sequential analysis steps are displayed from top to bottom. The pipeline inputs are depicted in blue color, steps are in green, and the end outputs are in red color. *Restriction enzyme cut site prediction step and the *type-II restriction enzymes list input are only applicable for MSRE-PCR and COBRA-PCR primers. **Bisulfite modification is only applicable for BSP, MSP, and COBRA methods. **Quality filter table file is optional; if user-defined primer selection criteria are not provided, then all primer pairs will be recorded in the final output summary table. ***Download and preparation of the reference sequence and annotation from UCSC genome browser step runs only once